Spring Runtime Error - Cannot resolve reference to bean 'entityManagerFactory' while setting constructor argument

Question

I've inherited a legacy Java app require JDK 7.

The app will compile, but I'm getting runtime errors which look like Hibernate entityManagerFactory issues.

The strange part is this app works on another developers machine. He even sent me his Tomcat directory, I have tried it on a Mac and on an Ubuntu machine. No matter where I run it, the runtime errors persist.

I think the problems is an init method in entityManagerFactory class,

Cannot resolve reference to bean 'entityManagerFactory' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in de.geoinfoffm.registry.persistence.PersistenceConfiguration: Invocation of init method failed; nested exception is java.lang.NullPointerException

pom.xml

PersistenceConfiguration Class:

 * Copyright (c) 2014, German Federal Agency for Cartography and Geodesy
 * All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions
 * are met:
 *     * Redistributions of source code must retain the above copyright
 *       notice, this list of conditions and the following disclaimer.

 *     * Redistributions in binary form must reproduce the above
 *       copyright notice, this list of conditions and the following
 *       disclaimer in the documentation and/or other materials
 *       provided with the distribution.

 *     * The names "German Federal Agency for Cartography and Geodesy",
 *       "Bundesamt für Kartographie und Geodäsie", "BKG", "GDI-DE",
 *       "GDI-DE Registry" and the names of other contributors must not
 *       be used to endorse or promote products derived from this
 *       software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE GERMAN
 * FEDERAL AGENCY FOR CARTOGRAPHY AND GEODESY BE LIABLE FOR ANY DIRECT,
 * INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
 * SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
 * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
 * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
 * IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
 * THE POSSIBILITY OF SUCH DAMAGE.
 */
package de.geoinfoffm.registry.persistence;

import java.sql.Connection;

import javax.annotation.PostConstruct;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.sql.DataSource;

import org.flywaydb.core.Flyway;
import org.flywaydb.core.api.MigrationInfo;
import org.flywaydb.core.api.MigrationInfoService;
import org.flywaydb.core.api.callback.FlywayCallback;
import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.ComponentScan;
import org.springframework.context.annotation.Configuration;
import org.springframework.core.env.Environment;
import org.springframework.dao.annotation.PersistenceExceptionTranslationPostProcessor;
import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
import org.springframework.orm.hibernate4.LocalSessionFactoryBean;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.JpaVendorAdapter;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.orm.jpa.vendor.HibernateJpaVendorAdapter;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.annotation.EnableTransactionManagement;

import de.bespire.LoggerFactory;
import de.geoinfoffm.registry.core.Repository;
import de.geoinfoffm.registry.core.configuration.RegistryConfiguration;
import de.geoinfoffm.registry.persistence.jpa.HibernateConfiguration;

/**
 * Spring configuration class for the persistence layer.
 * 
 * @author Florian Esser
 * 
 */
@ComponentScan(basePackages = { "de.bespire.registry", "de.geoinfoffm.registry" })
@Configuration
@EnableTransactionManagement
@EnableJpaRepositories(basePackages = { "de.bespire.registry", "de.geoinfoffm.registry" },
                       repositoryFactoryBeanClass = EntityBackendFactoryBean.class)
public class PersistenceConfiguration
{
    private static final Logger logger = LoggerFactory.make();

    @Autowired
    private Environment env;

    /**
     * Creates a {@link LocalContainerEntityManagerFactoryBean} that will handle the creation
     * of {@link EntityManager}s used by the {@link Repository}s of domain object {@link Repository}s.
     */
    @Autowired
    @Bean
    public LocalContainerEntityManagerFactoryBean entityManagerFactory(HibernateConfiguration hibernateConfiguration, RegistryConfiguration registryConfiguration, DatabaseSchemaMangementService schemaManagementService) {
        // Handle schema migration before creating the EntityManagerFactoryBean
        final String flywayMigration = hibernateConfiguration.additionalParameters().getProperty("flyway.migration", "false").toString().toLowerCase();
        if ("true".equalsIgnoreCase(flywayMigration)) {
            schemaManagementService.analyze();  
            schemaManagementService.migrate();
        }
        else if ("repair".equalsIgnoreCase(flywayMigration)) {
            schemaManagementService.repair();
        }
        else if ("repairAndMigrate".equalsIgnoreCase(flywayMigration)) {
            schemaManagementService.repairAndMigrate();
        }

        JpaVendorAdapter vendorAdapter = new HibernateJpaVendorAdapter();
        LocalContainerEntityManagerFactoryBean em = new LocalContainerEntityManagerFactoryBean();
        em.setDataSource(dataSource(hibernateConfiguration));
        em.setPackagesToScan(registryConfiguration.getBasePackages());
        em.setJpaVendorAdapter(vendorAdapter);
        em.setJpaProperties(hibernateConfiguration.additionalParameters());

        return em;
    }

    @Autowired
    @Bean
    public LocalSessionFactoryBean sessionFactory(HibernateConfiguration hibernateConfiguration, RegistryConfiguration registryConfiguration) {
        LocalSessionFactoryBean result = new LocalSessionFactoryBean();
        result.setDataSource(dataSource(hibernateConfiguration));
        result.setPackagesToScan(registryConfiguration.getBasePackages());

        return result;
    }

    /**
     * @return the {@link DataSource} for the application, based on the connection properties
     */
    @Autowired
    @Bean
    public DataSource dataSource(HibernateConfiguration hibernateConfiguration) {
        return hibernateConfiguration.dataSource();
    }

    /**
     * @return the {@link PlatformTransactionManager} for the application
     */
    @Autowired
    @Bean
    public PlatformTransactionManager transactionManager(HibernateConfiguration hibernateConfiguration, RegistryConfiguration registryConfiguration, DatabaseSchemaMangementService schemaService) {
        JpaTransactionManager transactionManager = new JpaTransactionManager();
        transactionManager.setEntityManagerFactory(entityManagerFactory(hibernateConfiguration, registryConfiguration, schemaService).getObject());

        return transactionManager;
    }

    /**
     * @return the {@link PersistenceExceptionTranslationPostProcessor} for the application
     */
    @Bean
    public PersistenceExceptionTranslationPostProcessor exceptionTranslation() {
        return new PersistenceExceptionTranslationPostProcessor();
    }

    @Autowired
    @Bean
    public DatabaseSchemaMangementService databaseSchemaMangementService(HibernateConfiguration hibernateConfiguration) {
        return new FlywayDatabaseSchemaManagementService(dataSource(hibernateConfiguration));
    }

}

Log file

INFO: 2 Spring WebApplicationInitializers detected on classpath
Feb 14, 2020 12:28:42 PM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
Feb 14, 2020 12:29:00 PM org.apache.catalina.core.StandardContext listenerStart
SEVERE: Exception sending context initialized event to listener instance of class [org.springframework.web.context.ContextLoaderListener]
org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'isoClientConfiguration': Unsatisfied dependency expressed through field 'sessionFactory'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'sessionFactory' defined in de.geoinfoffm.registry.persistence.PersistenceConfiguration: Unsatisfied dependency expressed through method 'sessionFactory' parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'hibernateConfiguration' defined in class path resource [org/iso/registry/client/configuration/web/IsoClientHibernateConfiguration.class]: Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'metaDataSourceAdvisor': Cannot resolve reference to bean 'methodSecurityMetadataSource' while setting constructor argument; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'org.springframework.security.config.annotation.method.configuration.GlobalMethodSecurityConfiguration': Unsatisfied dependency expressed through method 'setPermissionEvaluator' parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'securityConfiguration': Initialization of bean failed; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'userDetailsService': Unsatisfied dependency expressed through field 'userRepository'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'registryUserRepository': Cannot create inner bean '(inner bean)#7a511d1d' of type [org.springframework.orm.jpa.SharedEntityManagerCreator] while setting bean property 'entityManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '(inner bean)#7a511d1d': Cannot resolve reference to bean 'entityManagerFactory' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in de.geoinfoffm.registry.persistence.PersistenceConfiguration: Invocation of init method failed; nested exception is java.lang.NullPointerException
    at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:588)
    at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:88)
    at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessPropertyValues(AutowiredAnnotationBeanPostProcessor.java:366)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1272)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:553)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
    at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:372)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1181)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1075)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:513)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)
    at org.springframework.context.support.AbstractApplicationContext.initMessageSource(AbstractApplicationContext.java:713)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:531)
    at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:443)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:325)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5195)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5720)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:1016)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:992)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:639)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1127)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:2020)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
Caused by: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'sessionFactory' defined in de.geoinfoffm.registry.persistence.PersistenceConfiguration: Unsatisfied dependency expressed through method 'sessionFactory' parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'hibernateConfiguration' defined in class path resource [org/iso/registry/client/configuration/web/IsoClientHibernateConfiguration.class]: Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'metaDataSourceAdvisor': Cannot resolve reference to bean 'methodSecurityMetadataSource' while setting constructor argument; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'org.springframework.security.config.annotation.method.configuration.GlobalMethodSecurityConfiguration': Unsatisfied dependency expressed through method 'setPermissionEvaluator' parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'securityConfiguration': Initialization of bean failed; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'userDetailsService': Unsatisfied dependency expressed through field 'userRepository'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'registryUserRepository': Cannot create inner bean '(inner bean)#7a511d1d' of type [org.springframework.orm.jpa.SharedEntityManagerCreator] while setting bean property 'entityManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '(inner bean)#7a511d1d': Cannot resolve reference to bean 'entityManagerFactory' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in de.geoinfoffm.registry.persistence.PersistenceConfiguration: Invocation of init method failed; nested exception is java.lang.NullPointerException
    at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:749)
    at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:467)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1181)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1075)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:513)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)
    at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:208)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1138)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1066)
    at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:585)
    ... 36 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'hibernateConfiguration' defined in class path resource [org/iso/registry/client/configuration/web/IsoClientHibernateConfiguration.class]: Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'metaDataSourceAdvisor': Cannot resolve reference to bean 'methodSecurityMetadataSource' while setting constructor argument; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'org.springframework.security.config.annotation.method.configuration.GlobalMethodSecurityConfiguration': Unsatisfied dependency expressed through method 'setPermissionEvaluator' parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'securityConfiguration': Initialization of bean failed; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'userDetailsService': Unsatisfied dependency expressed through field 'userRepository'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'registryUserRepository': Cannot create inner bean '(inner bean)#7a511d1d' of type [org.springframework.orm.jpa.SharedEntityManagerCreator] while setting bean property 'entityManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '(inner bean)#7a511d1d': Cannot resolve reference to bean 'entityManagerFactory' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in de.geoinfoffm.registry.persistence.PersistenceConfiguration: Invocation of init method failed; nested exception is java.lang.NullPointerException
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:564)
    at 

Update - Looks like the problem is base packages are not found for this project.

The class that handles getting base packages - getBasePackages() Of course, I don't know why this project is not finding base packages on my dev instance.

Answer 1

You have a nested NullPointerException in what looks like your PersistenceConfiguration class

Error creating bean with name 'entityManagerFactory' defined in de.geoinfoffm.registry.persistence.PersistenceConfiguration: Invocation of init method failed; nested exception is java.lang.NullPointerException

Consider posting your code as well if the source of the NPE is not obvious.

Answer 2

There is a problem with existing code and handling string arrays.

Nothing wrong with Spring or Hibernate or pom file configurations.